I don’t have the option to transfer files from an FTP server to my history on Galaxy.org. Unfortunately, Paste/Fetch Data isn’t working either and is displaying an error. I’m trying to transfer files directly from my computer, but it’s taking a very long time. Unfortunately, I can’t use other servers because this is the only one that has the cow genome I need for mapping my samples. How can I resolve the issue with transferring files via FTP?
Welcome @Robert_Rekawiecki
Are you still having this problem now?
To FTP data into Galaxy, there are two criteria
- you need to be logged into a confirmed account at the server
- that server needs to support FTP
The UseGalaxy* servers do not support FTP transfers anymore but other Galaxy servers might. If you are working with very large batches of data and workflows, perhaps interacting with the API via scripts, there is another utility you can try instead. You can also attach your own storage and avoid Upload/Download steps entirely!
The expanded API methods, and FTP (if the server you are working at still supports it) are covered here:
- GitHub - galaxyproject/galaxy-upload: Galaxy Upload Utility for the CLI · GitHub
- FAQ: Upload many files (>10) via FTP
With data storage options covered here:
Related (native storage) → How to access your Self Serve extended data storage at UseGalaxy servers! - #2 by jennaj
Since you are working at UseGalaxy.org, you’ll need to try one of the other methods. Remember to stay connected to the server throughout the transfers (same as for FTP). The Upload tool supports resuming if the connection drops for some reason.
Hope this explains your observations, but please let us know or if you have any followup questions! 
Usegalaxy.eu you can upload vis FTP
To upload use "your email"@ftp.usegalaxy.eu
This uploads to the “Choose from repository” button on your uploads, your upload will be in the top link.
Though currently I can’t upload or transfer anything from usegalaxy.eu
Yes, FTP was previously available at the UseGalaxy.eu server but I think that has been toggled off for all UseGalaxy now. We can let @wm75 and @igor comment. It is definitely not possible at UseGalaxy.org (and will not be for the immediate term).
FTP doesn’t gain anything that the Upload tool doesn’t manage the same way for the technical parts of transfer (progress, resume). So I am going to recommend everyone use this directly. Then for batch programmatic access, the Upload Utility is available (fully command line).
Hi @jennaj
yes, Galaxy Australia does not support FTP for years.
Many mapping tools in Galaxy support reference genomes from a history.
Generally, uploads via web interface or URL are fast, and bottleneck might be in data transfer from a local computer/storage. Check your upload speed. Try different connection options (wireless, LAN). By any chance, do you keep the files on external storage?
What error do you see with Paste/Fetch Data? Any chance your links are password protected or data source is behind firewall?
Kind regards,
Igor