Frequently Asked Questions
What should I do special if on usegalaxy.be?
Note for anyone trying to follow the tutorial on usegalaxy.be:
In step 3 of the hands-on section of setting up the sars-cov-2 analysis bot, when suggested to run
planemo run vcf2lineage.ga vcf2lineage-job.yml --profile planemo-tutorial --history_name "vcf2lineage test"
please use directly the workflow ID
vcf2lineage.ga. This ID points to a public workflow that’s using the version of the pangolin tool installed on usegalaxy.be`.
Can't find one of the tools for this tutorial?
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.
Running into an error?
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!
- In the GTN Gitter Channel
- In the Galaxy Gitter Channel
- Browse the Galaxy Help Forum to see if others have encountered the same problem before (or post your question).
- When asking for help, it is useful to share a link to your history