Hello,
You are missing dependencies that Galaxy needs.
I can reproduce this in a Galaxy release version 19.01
that was initialized/started up without using a Python virtualenv
(a Conda virtualenv
was used, because I have conda installed on my computer, and you probably do, too). The beginning of the startup log when you first initialized Galaxy notes if a Python versus Conda venv
is used.
Other things could potentially go wrong when using Galaxy this way. There is probably some method to fix all the potentially missing dependencies but this would require but I don’t know the scope for this release and the developers always state to just start over using Python.
Please see this Q&A from yesterday that covers how to make the correction: Error when trying to run Galaxy on MacOs
It is important to note that this is only a first step – my test involved loading up a fairly small fasta file (successfully), launching IGV, and then clicking on the “IGV local” link. Same exact error as you report (from IGV). Larger fasta files (over ~150 MB) also failed but with a different reason, even though I was testing in a Conda venv
build Galaxy. So, the data in the tutorial might still be too large for your local Galaxy (with default configuration under Conda venv
) but you can test that out. This would be the starting place for recreating the error data (the error dataset you show might resolve – it looks to be due to a missing dependency) and also going further with more administrative customization should you decide to go that route.