A Short Introduction to Galaxy
Contributors
Questions
What is Galaxy?
Why should I use Galaxy?
How do I use Galaxy?
How can I connect with the Galaxy Community?
What is Galaxy?
Speaker Notes
What is Galaxy?
Data Intensive analysis for everyone
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- Data Analysis platform
- Web-based
- Easy to use
-
Free and Open Source
- Many tools (~8000)
- Popular (>10.000 publications)
- Extensive tutorials available
]
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.footnote[Homepage: galaxyproject.org]
Speaker Notes
- Galaxy is a web based data analysis platform.
- It is easy to use, and completely free.
- Galaxy offers over eight thousand analysis tools.
- Galaxy is widely used. It currently has over ten thousand publications.
Why use Galaxy?
- It’s easy!
- No installation, all you need is a browser.
- No complex commands, just point and click!
- Makes your research reproducible
- Galaxy keeps track of all analysis details
- Cross-domain: bioinformatics, chemistry, ecology, climate science, ..
Speaker Notes
- Data analysis can be very complex.
- It often requires specialized programming knowledge or command line skills.
- Galaxy makes this a lot easier by providing a web-based user interface to popular data analysis tools.
- This means you don’t have to install anything, just open your browser and go to Galaxy.
- Galaxy also helps you make your research reproducible by keeping track of your analysis steps.
- Galaxy supports many different scientific domains.
How do I use Galaxy?
Speaker Notes
- How do I use Galaxy?
Find a Galaxy server
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The Big Three: Galaxy Main (usegalaxy.org), Galaxy Europe (usegalaxy.eu), Galaxy Australia (usegalaxy.org.au)
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- Many other smaller, often domain-specific Galaxies available
- List of all public Galaxies (125+): galaxyproject.org/use
Speaker Notes
- There are three main Galaxy servers: Galaxy Main, Galaxy Europe, and Galaxy Australia.
- These three Galaxies have the biggest teams behind them, and offer the most tools and resources.
- You can register an account for free on any of these servers.
- In addition, there are many smaller Galaxy servers to choose from.
- Many of these are domain specific. For example, Galaxy Proteomics focuses on proteomics tools and workflows.
- A lot of universities and other institutions have local private servers.
The Galaxy Interface
- Three main panels
- Left: Available Tools
- Middle: View your data and run tools
- Right: Full record of your analysis history
Speaker Notes
- The Galaxy user interface consists of three main parts.
- On the left is the list of available tools.
- In the middle panel you will run your analysis tools and view your data and results.
- On the right is a full record of your analysis history.
Uploading data
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Upload from your computer
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Import files from URL
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Import from public data stores
- UCSC, NCBI, ENA, many more..
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Speaker Notes
- The first step of an analysis is to get your data into Galaxy.
- This can be done in several ways.
- You can upload files from your computer.
- Or you can enter an Internet URL, and Galaxy will download the data for you.
- Furthermore, Galaxy can import data directly from many online data stores such as UCSC, NCBI, and many more.
History
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The history collects all the files of your analysis
- Three buttons
- galaxy-eye View the file
- galaxy-pencil Edit attributes
- e.g. change name
- galaxy-cross Delete file
- Click to expand
- file information
- format, size, ..
- file preview
- file options
- download, visualize, ..
- file information
]
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Speaker Notes
- All files you upload will appear in your history.
- There are 3 button on each dataset in your history.
- The eye icon lets you view the dataset. This will show up in the middle panel of Galaxy.
- The pencil icon allows you to edit the attributes of the file. For example you can change the file name here.
- The cross icon lets you delete the dataset from your history.
- You can also click on the dataset to expand it. This will show more information and more options.
Finding a tool
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- Explore tool panel sections
- Enter name in Tool search box ]
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- galaxy-star Star you favorite tools to make them easier to find
Speaker Notes
- After your data is uploaded, you are ready to run tools.
- You can find tools by exploring the tool list on the left.
- If you already know the name of the tool you want to use, you can enter this in the search box at the top of the tool panel.
- If you have found a tool you like, you can add it to your favorites by clicking the star at the top of the tool.
Running a tool
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- Choose input files
- Set tool parameters
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Execute
- Below tool form:
- Help information
- Tool citation
]
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Speaker Notes
- When you click on a tool, it will show up in the middle panel.
- Here you can select your input files and set the parameters for the tool.
- Then you can hit the Execute button to start the tool.
- Older versions of a tool are usually kept available to ensure reproducibility.
Analysis Results
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Tool outputs are added to the history
- Different dataset states
- waiting , running , success, failed
- Expand for more options
- galaxy-save Download dataset
- galaxy-info Information about tool run
- galaxy-refresh Reload tool with the same parameters
- galaxy-barchart Visualize dataset
- Red dataset?
- galaxy-bug Click Bug icon
- view error message
- submit error report ]
- galaxy-bug Click Bug icon
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Speaker Notes
- The results of the analysis will be added to your history.
- You will see these output files go through various states.
- When a dataset is grey, it means it is waiting to run.
- When it turns orange, it means the tool is running.
- When the tool is finished, the outputs will turn green if the tool ran successfully.
- You can then click on the history item to get more information and options.
- For example, you can download the file to your computer.
- Or you can reload the tool with the same parameters.
- There is also an option to visualize your data.
- If there was a problem with the tool, it will turn red.
- You can click on the bug icon to view the error message or submit a error report to the Galaxy administrators.
Visualisations
- Galaxy has many options to visualize data
Speaker Notes
- Galaxy offers several ways to visualize your datasets depending on their format.
- For example, protein PDB data can be seen in a 3D viewer.
Multiple Analyses
- Starting a new analysis? Create a new history new-history
- You can have as many histories as you want
- Overview of all your histories galaxy-history
- Good names for your histories help to keep track of your analyses
Speaker Notes
- When you want to start a new analysis, create a new history using the plus icon at the top of the history panel.
- You can always go back to an old history, and there is no limit on the number of histories you can create.
- An overview of your histories is available where you can easily copy files around.
- Copying datasets instead of re-uploading them let you save on your quota.
- Giving your histories good names will help you keep track of your analyses’
Workflows
- Run end-to-end analyses with one click
- Extract from a history
- Build manually with workflow editor
- Import a shared workflow
Speaker Notes
- Workflows let you run your analyses very easily by connecting tools’ outputs and inputs.
- There are multiple ways to create a workflow.
- Workflows can be automatically extracted from a history.
- This means you perform the analysis manually once, and then can easily repeat it on different input data.
- You can also build workflows by hand using the workflow editor to connect the tools.
- Or you can import a workflow somebody else has shared with you.
Sharing
- You can share everything you do in Galaxy
- Histories, Workflows, Visualizations
- Sharing options
- Share with specific users
- Share via link
- Publish to make it visible to everybody
Speaker Notes
- Everything you do in Galaxy can be shared.
- You can share your history, your workflow, and your visualizations.
- There are different ways to share your work.
- You can either share it with specific Galaxy users.
- Or you can get a share link that you can send to anybody.
- If you publish your work, it will be visible to everybody.
Learning Galaxy
- Galaxy Training Materials (training.galaxyproject.org)
Speaker Notes
- If you would like to learn more about Galaxy, there are a large number of tutorials available.
- These tutorials cover a wide range of scientific domains.
Getting Help
-
Help Forum (help.galaxyproject.org)
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Chat on Matrix
- Main Chat
- Galaxy Training Chat
- Many more channels (scientific domains, developers, admins)
Speaker Notes
- If you get stuck, there are ways to get help.
- You can ask your questions on the help forum.
- Or you can chat with the community on Matrix.
Join an event
- Many Galaxy events across the globe
- Event Horizon: galaxyproject.org/events
Speaker Notes
- There are frequent Galaxy events all around the world.
- You can find upcoming events on the Galaxy Event Horizon.
Key Points
- Galaxy lets you perform complex data analysis right from your browser
- These analyses are *reproducible*; Galaxy keeps track of all the details of your analysis
- Galaxy has a very large and active user community
- There are many training materials available to learn Galaxy