Frequently Asked Questions
Hands-on: Launch RStudio
Depending on which server you are using, you may be able to run RStudio directly in Galaxy. If that is not available, RStudio Cloud can be an alternative.
- Open the Rstudio tool tool by clicking here to launch RStudio
- Click Run Tool
- The tool will start running and will stay running permanently
- Click on the “User” menu at the top and go to “Active InteractiveTools” and locate the RStudio instance you started.
If RStudio is not available on the Galaxy instance:
- Register for RStudio Cloud, or login if you already have an account
- Create a new project
Hands-on: Stop RStudio
When you have finished your R analysis, it’s time to stop RStudio.
- First, save your work into Galaxy, to ensure reproducibility:
- You can use
gx_put(filename)to save individual files by supplying the filename
- You can use
gx_save()to save the entire analysis transcript and any data objects loaded into your environment.
- Once you have saved your data, you can proceed in 2 different ways:
- Deleting the corresponding history dataset named
RStudioand showing a “in progress state”, so yellow, OR
- Clicking on the “User” menu at the top and go to “Active InteractiveTools” and locate the RStudio instance you started, selecting the corresponding box, and finally clicking on the “Stop” button at the bottom.
To use the tools installed and available on the Galaxy server:
- At the top of the left tool panel, type in a tool name or datatype into the tool search box.
- Shorter keywords find more choices.
- Tools can also be directly browsed by category in the tool panel.
If you can’t find a tool you need for a tutorial on Galaxy, please:
- Check that you are using a compatible Galaxy server
- Navigate to the overview box at the top of the tutorial
- Find the “Supporting Materials” section
- Check “Available on these Galaxies”
- If your server is not listed here, the tutorial is not supported on your Galaxy server
- You can create an account on one of the supporting Galaxies
- Use the Tutorial mode feature
- Open your Galaxy server
- Click on the curriculum icon on the top menu, this will open the GTN inside Galaxy.
- Navigate to your tutorial
- Tool names in tutorials will be blue buttons that open the correct tool for you
- Note: this does not work for all tutorials (yet)
- Still not finding the tool?
- Ask help in Gitter.
When something goes wrong in Galaxy, there are a number of things you can do to find out what it was. Error messages can help you figure out whether it was a problem with one of the settings of the tool, or with the input data, or maybe there is a bug in the tool itself and the problem should be reported. Below are the steps you can follow to troubleshoot your Galaxy errors.
- Expand the red history dataset by clicking on it.
- Sometimes you can already see an error message here
View the error message by clicking on the bug icon galaxy-bug
- Check the logs. Output (stdout) and error logs (stderr) of the tool are available:
- Expand the history item
- Click on the details icon
- Scroll down to the Job Information section to view the 2 logs:
- Tool Standard Output
- Tool Standard Error
- For more information about specific tool errors, please see the Troubleshooting section
- Submit a bug report! If you are still unsure what the problem is.
- Click on the bug icon galaxy-bug
- Write down any information you think might help solve the problem
- See this FAQ on how to write good bug reports
- Click galaxy-bug Report button
- Ask for help!