I’m encountering an issue with the Galaxy web interface and would appreciate some guidance. In the history section, each Galaxy dataset contains a text box filled with the tool output, consisting of “Tool Standard Output” followed by “Tool Standard Error,” as visible in the “Dataset Information” panel.
As a developer, I’ve included relevant information in the stdout for users and placed debugging logs in the stderr to assist developers in case of tool-related issues. However, I’ve noticed that these stderr logs, intended for developers, can be confusing for users.
My question is: Is there a way to hide the stderr output in the dataset textbox while retaining it in the Dataset Information panel?
Any help or suggestions would be greatly appreciated. Thank you!
Not that I know of with an existing flag or configuration option, but I suppose you could custom configure your own instance to do that. I can’t help with that but someone else might be able to.
One complication is that some community tool wrapper authors do push relevant information into stderr… and that stderr is pushed to job info in part (as part of the tool wrapper with a regex against the full log).
So, what you are seeing inside the expanded data is actually a third log: “Job Information” . Find this by clicking on the pencil icon. A user can edit this field too. That is on purpose since it is a multi-use field for user notes, key parts of logs (redundant visibility), various warnings, and sometimes statistics or data metrics.