I am trying to upload fastq.gz sequence files from Globus.
I pasted the url into the galaxy paste/fetch data screen. Things seem to be uploading ok until I receive this error at the end.
The uploaded file contains invalid HTML content.
I pasted the url into the galaxy paste/fetch data screen. Things seem to be uploading ok until I receive this error at the end.
The uploaded file contains invalid HTML content.
Welcome @Lzprry
The only “rules” for Galaxy are that a link is public, and that it is directly to a file (not a redirect). It is also best to leave all the settings in the Upload tool at the defaults. Please see for more → Getting Data into Galaxy
It sounds like the file is public from the description but I am wondering if the link is pointing to the actual file itself, or if it is a redirect. If a redirect, and not the actual file itself, an “HTML” error will be reported by the Upload tool at a public Galaxy server (certain) and possibly at other Galaxy servers (depends on how the administrator configured the server) but it still wouldn’t be the data itself loaded into the history.
The other option is that the link is dead and the HTML is coming from a 404 browser error.
Can you download the file? Meaning, is it really accessible? To get data out of certain environments over into Galaxy, sometimes a clear, direct link isn’t available from that application, and an intermediate download step is needed. You could also move the file over to a host server with a clear/direct link, or explore some of the alternative cloud links hosted at the UseGalaxy.eu server (only, for now) – find these under the User → Preferences → Manage Information view.
Hope this helps! 
Thank you. I am able to download the file. I can upload it to galaxy from my local machine. Globus says that the URL is a direct link, but I can’t get past the HTML error. I will explore options for an intermediate download step to then upload to galaxy. Thanks for your quick reply!
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HI @Lzprry
I’m glad you have a work around.
However, downloading data is a pain! If the link is actually public and direct, I’m curious. Maybe we can adjust something ourselves or collaborate with Globus.
If you could post back a link in free text, any dataset but really tiny is best, we can troubleshoot what exactly the problem is. Please make sure that the URL still generates the error you are concerned about so I can create a small test to share with the developers. The server where you were trying this might matter too (in particular, the version of Galaxy running), so please also share the URL for that (the base URL from the top of your browser window).
Thanks for the follow up! Actual use cases help us to improve the application. 